Multi-species integration of miRNA binding site data to improve target prediction accuracy for synaptic miRNAs

Micro-RNAs (miRNA) are thought to play an important role in the modulation of synaptic strength during activity dependent synaptic plasticity by regulating protein synthesis. Identifying the target mRNAs of the miRNAs involved is a crucial part of understanding how this regulation takes place, but is confounded by the small size and sequence variability of miRNA binding sites (typically as few as 6-8 nucleotides). Recent studies have attempted to improve the identification of miRNA targets by isolating miRNAs and their mRNA targets as part of the RISC complex using antibodies raised against the Arg2 protein in both human and mice and sequencing the resulting RNA pools. We used data produced by this technique, in addition to other cross-species information, to produce a classification procedure for improving microRNA target prediction in the rat.